Bioinformatics 2018
(Mon 8 Jan 2018 - Tue 18 Dec 2018)
[ Back to start of the programme ]
July 2018
| Thu 12 |
This course provides a practical introduction to the writing of Python programs for the complete novice. Participants are lead through the core aspects of Python illustrated by a series of example programs. Upon completion of the course, attentive participants will be able to write simple Python programs and customize more complex code to fit their needs. Course materials are available here. Please note that the content of this course has recently been updated. This course now mostly focuses on core concepts including Python syntax, data structures and reading/writing files. Functions and modules are now the focus of a new 1-day course, Working with Python: functions and modules. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here. |
| Fri 13 |
This course provides a practical introduction to the writing of Python programs for the complete novice. Participants are lead through the core aspects of Python illustrated by a series of example programs. Upon completion of the course, attentive participants will be able to write simple Python programs and customize more complex code to fit their needs. Course materials are available here. Please note that the content of this course has recently been updated. This course now mostly focuses on core concepts including Python syntax, data structures and reading/writing files. Functions and modules are now the focus of a new 1-day course, Working with Python: functions and modules. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here. |
| Mon 16 |
Variant Discovery with GATK4
Finished
This workshop will focus on the core steps involved in calling variants with the Broad’s Genome Analysis Toolkit, using the “Best Practices” developed by the GATK team. You will learn why each step is essential to the variant discovery process, what are the operations performed on the data at each step, and how to use the GATK tools to get the most accurate and reliable results out of your dataset. In the course of this workshop, we highlight key functionalities such as the germline GVCF workflow for joint variant discovery in cohorts, somatic variant discovery using MuTect2, and copy number variation discovery using GATK-CNV. All analyses are demonstrated using GATK version 4. Finally, we demonstrate the use of pipelining tools to assemble and execute GATK workflows. The workshop covers basic genomics, all currently supported Best Practices pipelines as well as pipelining with WDL/Cromwell/FireCloud. This includes the logic of the major pipelines, file formats and data transformations involved, and hands-on operation of the tools using goal-oriented exercises.
Please note that this workshop is focused on human data analysis. The majority of the materials presented does apply equally to non-human data, and we will address some questions regarding adaptations that are needed for analysis of non-human data, but we will not go into much detail on those points. Please note that if you are not eligible for a University of Cambridge Raven account you will need to Book or register Interest by linking here. |
| Tue 17 |
Variant Discovery with GATK4
Finished
This workshop will focus on the core steps involved in calling variants with the Broad’s Genome Analysis Toolkit, using the “Best Practices” developed by the GATK team. You will learn why each step is essential to the variant discovery process, what are the operations performed on the data at each step, and how to use the GATK tools to get the most accurate and reliable results out of your dataset. In the course of this workshop, we highlight key functionalities such as the germline GVCF workflow for joint variant discovery in cohorts, somatic variant discovery using MuTect2, and copy number variation discovery using GATK-CNV. All analyses are demonstrated using GATK version 4. Finally, we demonstrate the use of pipelining tools to assemble and execute GATK workflows. The workshop covers basic genomics, all currently supported Best Practices pipelines as well as pipelining with WDL/Cromwell/FireCloud. This includes the logic of the major pipelines, file formats and data transformations involved, and hands-on operation of the tools using goal-oriented exercises.
Please note that this workshop is focused on human data analysis. The majority of the materials presented does apply equally to non-human data, and we will address some questions regarding adaptations that are needed for analysis of non-human data, but we will not go into much detail on those points. Please note that if you are not eligible for a University of Cambridge Raven account you will need to Book or register Interest by linking here. |
| Wed 18 |
Variant Discovery with GATK4
Finished
This workshop will focus on the core steps involved in calling variants with the Broad’s Genome Analysis Toolkit, using the “Best Practices” developed by the GATK team. You will learn why each step is essential to the variant discovery process, what are the operations performed on the data at each step, and how to use the GATK tools to get the most accurate and reliable results out of your dataset. In the course of this workshop, we highlight key functionalities such as the germline GVCF workflow for joint variant discovery in cohorts, somatic variant discovery using MuTect2, and copy number variation discovery using GATK-CNV. All analyses are demonstrated using GATK version 4. Finally, we demonstrate the use of pipelining tools to assemble and execute GATK workflows. The workshop covers basic genomics, all currently supported Best Practices pipelines as well as pipelining with WDL/Cromwell/FireCloud. This includes the logic of the major pipelines, file formats and data transformations involved, and hands-on operation of the tools using goal-oriented exercises.
Please note that this workshop is focused on human data analysis. The majority of the materials presented does apply equally to non-human data, and we will address some questions regarding adaptations that are needed for analysis of non-human data, but we will not go into much detail on those points. Please note that if you are not eligible for a University of Cambridge Raven account you will need to Book or register Interest by linking here. |
| Thu 19 |
Variant Discovery with GATK4
Finished
This workshop will focus on the core steps involved in calling variants with the Broad’s Genome Analysis Toolkit, using the “Best Practices” developed by the GATK team. You will learn why each step is essential to the variant discovery process, what are the operations performed on the data at each step, and how to use the GATK tools to get the most accurate and reliable results out of your dataset. In the course of this workshop, we highlight key functionalities such as the germline GVCF workflow for joint variant discovery in cohorts, somatic variant discovery using MuTect2, and copy number variation discovery using GATK-CNV. All analyses are demonstrated using GATK version 4. Finally, we demonstrate the use of pipelining tools to assemble and execute GATK workflows. The workshop covers basic genomics, all currently supported Best Practices pipelines as well as pipelining with WDL/Cromwell/FireCloud. This includes the logic of the major pipelines, file formats and data transformations involved, and hands-on operation of the tools using goal-oriented exercises.
Please note that this workshop is focused on human data analysis. The majority of the materials presented does apply equally to non-human data, and we will address some questions regarding adaptations that are needed for analysis of non-human data, but we will not go into much detail on those points. Please note that if you are not eligible for a University of Cambridge Raven account you will need to Book or register Interest by linking here. |
| Fri 20 |
Using the Ensembl Genome Browser
Finished
The Ensembl Project provides a comprehensive and integrated source of annotation of, mainly vertebrate, genome sequences. This workshop offers a comprehensive practical introduction to the use of the Ensembl genome browser as well as essential background information. This course will focus on the vertebrate genomes in Ensembl, however much of what will be covered is also applicable to the non-vertebrates (plants, bacteria, fungi, metazoa and protists) in Ensembl Genomes. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here. |
| Mon 30 |
CRUK: Image Analysis with Fiji
Finished
Fiji/ImageJ is a popular open-source image analysis software application. This course will briefly cover introductory aspects of image processing and analysis theory, but will focus on practical sessions where participants will gain hands on experience with Fiji. This course is run by the CRUK CI Light microscopy core facility. Please note that if you are not eligible for a University of Cambridge Raven account you will need to Book or register Interest by linking here. |
September 2018
| Mon 3 |
The aim of this course is to familiarize the participants with the primary analysis of RNA-seq data. This course starts with a brief introduction to RNA-seq and discusses quality control issues. Next, we will present the alignment step, quantification of expression and differential expression analysis. For downstream analysis we will focus on tools available through the Bioconductor project for manipulating and analysing bulk RNA-seq. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here. |
| Tue 4 |
The aim of this course is to familiarize the participants with the primary analysis of RNA-seq data. This course starts with a brief introduction to RNA-seq and discusses quality control issues. Next, we will present the alignment step, quantification of expression and differential expression analysis. For downstream analysis we will focus on tools available through the Bioconductor project for manipulating and analysing bulk RNA-seq. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here. |
| Wed 5 |
The aim of this course is to familiarize the participants with the primary analysis of RNA-seq data. This course starts with a brief introduction to RNA-seq and discusses quality control issues. Next, we will present the alignment step, quantification of expression and differential expression analysis. For downstream analysis we will focus on tools available through the Bioconductor project for manipulating and analysing bulk RNA-seq. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here. |
| Thu 6 |
This course provides a practical introduction to the writing of Python programs for the complete novice. Participants are lead through the core aspects of Python illustrated by a series of example programs. Upon completion of the course, attentive participants will be able to write simple Python programs and customize more complex code to fit their needs. Course materials are available here. Please note that the content of this course has recently been updated. This course now mostly focuses on core concepts including Python syntax, data structures and reading/writing files. Functions and modules are now the focus of a new 1-day course, Working with Python: functions and modules. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here. |
| Fri 7 |
This course provides a practical introduction to the writing of Python programs for the complete novice. Participants are lead through the core aspects of Python illustrated by a series of example programs. Upon completion of the course, attentive participants will be able to write simple Python programs and customize more complex code to fit their needs. Course materials are available here. Please note that the content of this course has recently been updated. This course now mostly focuses on core concepts including Python syntax, data structures and reading/writing files. Functions and modules are now the focus of a new 1-day course, Working with Python: functions and modules. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here. |
| Mon 10 |
Statistics for Biologists in R
Finished
This course is intended to provide a strong foundation in practical statistics and data analysis using the R software environment. The underlying philosophy of the course is to treat statistics as a practical skill rather than as a theoretical subject and as such the course focuses on methods for addressing real-life issues in the biological sciences using the R software package. In this course we explore classical statistical analysis techniques starting with simple hypothesis testing and building up to multiple linear regression. The focus of the course is on practical implementation of these techniques and developing robust statistical analysis skills rather than on the underlying statistical theory. After the course you should feel confident to be able to select and implement common statistical techniques using R and moreover know when, and when not, to apply these techniques. This event is supported by the BBSRC Strategic Training Awards for Research Skills (STARS) grant (BB/P022766/1). Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here. |
|
CRUK: Image Analysis with Fiji
Finished
Fiji/ImageJ is a popular open-source image analysis software application. This course will briefly cover introductory aspects of image processing and analysis theory, but will focus on practical sessions where participants will gain hands on experience with Fiji. This course is run by the CRUK CI Light microscopy core facility. Please note that if you are not eligible for a University of Cambridge Raven account you will need to Book or register Interest by linking here. |
|
| Tue 11 |
Statistics for Biologists in R
Finished
This course is intended to provide a strong foundation in practical statistics and data analysis using the R software environment. The underlying philosophy of the course is to treat statistics as a practical skill rather than as a theoretical subject and as such the course focuses on methods for addressing real-life issues in the biological sciences using the R software package. In this course we explore classical statistical analysis techniques starting with simple hypothesis testing and building up to multiple linear regression. The focus of the course is on practical implementation of these techniques and developing robust statistical analysis skills rather than on the underlying statistical theory. After the course you should feel confident to be able to select and implement common statistical techniques using R and moreover know when, and when not, to apply these techniques. This event is supported by the BBSRC Strategic Training Awards for Research Skills (STARS) grant (BB/P022766/1). Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here. |
| Wed 12 |
R is a highly-regarded, free, software environment for statistical analysis, with many useful features that promote and facilitate reproducible research. In this course, we give an introduction to the R environment and explain how it can be used to import, manipulate and analyse tabular data. After the course you should feel confident to start exploring your own dataset using the materials and references provided. The course website providing links to the course materials is here. Please note that although we will demonstrate how to perform statistical analysis in R, we will not cover the theory of statistical analysis in this course. Those seeking an in-depth explanation of how to perform and interpret statistical tests are advised to see the list of Related courses. Moreover, those with some programming experience in other languages (e.g. Python, Perl) might wish to attend the follow-on Data Analysis and Visualisation in R course. This event is supported by the BBSRC Strategic Training Awards for Research Skills (STARS) grant (BB/P022766/1). Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here. |
| Thu 13 |
R is a highly-regarded, free, software environment for statistical analysis, with many useful features that promote and facilitate reproducible research. In this course, we give an introduction to the R environment and explain how it can be used to import, manipulate and analyse tabular data. After the course you should feel confident to start exploring your own dataset using the materials and references provided. The course website providing links to the course materials is here. Please note that although we will demonstrate how to perform statistical analysis in R, we will not cover the theory of statistical analysis in this course. Those seeking an in-depth explanation of how to perform and interpret statistical tests are advised to see the list of Related courses. Moreover, those with some programming experience in other languages (e.g. Python, Perl) might wish to attend the follow-on Data Analysis and Visualisation in R course. This event is supported by the BBSRC Strategic Training Awards for Research Skills (STARS) grant (BB/P022766/1). Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here. |
| Fri 14 |
This course introduces some relatively new additions to the R programming language: dplyr and ggplot2. In combination these R packages provide a powerful toolkit to make the process of manipulating and visualising data easy and intuitive. Materials for this course can be found here. The training room is located on the first floor and there is currently no level access. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here. |
| Mon 24 |
Data Carpentry in R
Finished
In many domains of research the rapid generation of large amounts of data is fundamentally changing how research is done. The deluge of data presents great opportunities, but also many challenges in managing, analyzing and sharing data. Data Carpentry workshops are designed to teach basic concepts, skills and tools for working more effectively with data, using a combination of tools with a main focus in R. The workshop is aimed at researchers in the life sciences at all career stages and is designed for learners with little to no prior knowledge of programming, shell scripting, or command line tools. This course is organized in collaboration with ElixirUK and the Software Sustainability Institute. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here. |
| Tue 25 |
Data Carpentry in R
Finished
In many domains of research the rapid generation of large amounts of data is fundamentally changing how research is done. The deluge of data presents great opportunities, but also many challenges in managing, analyzing and sharing data. Data Carpentry workshops are designed to teach basic concepts, skills and tools for working more effectively with data, using a combination of tools with a main focus in R. The workshop is aimed at researchers in the life sciences at all career stages and is designed for learners with little to no prior knowledge of programming, shell scripting, or command line tools. This course is organized in collaboration with ElixirUK and the Software Sustainability Institute. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here. |
| Wed 26 |
An Introduction to Machine Learning
Finished
Machine learning gives computers the ability to learn without being explicitly programmed. It encompasses a broad range of approaches to data analysis with applicability across the biological sciences. Lectures will introduce commonly used algorithms and provide insight into their theoretical underpinnings. In the practicals students will apply these algorithms to real biological data-sets using the R language and environment. Please be aware that the course syllabus is currently being updated following feedback from the last event; therefore the agenda below will be subjected to changes. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here. |
| Thu 27 |
An Introduction to Machine Learning
Finished
Machine learning gives computers the ability to learn without being explicitly programmed. It encompasses a broad range of approaches to data analysis with applicability across the biological sciences. Lectures will introduce commonly used algorithms and provide insight into their theoretical underpinnings. In the practicals students will apply these algorithms to real biological data-sets using the R language and environment. Please be aware that the course syllabus is currently being updated following feedback from the last event; therefore the agenda below will be subjected to changes. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here. |
| Fri 28 |
An Introduction to Machine Learning
Finished
Machine learning gives computers the ability to learn without being explicitly programmed. It encompasses a broad range of approaches to data analysis with applicability across the biological sciences. Lectures will introduce commonly used algorithms and provide insight into their theoretical underpinnings. In the practicals students will apply these algorithms to real biological data-sets using the R language and environment. Please be aware that the course syllabus is currently being updated following feedback from the last event; therefore the agenda below will be subjected to changes. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here. |
October 2018
| Wed 17 |
Introduction to Unix shell
Finished
This course offers an introduction to working with Linux. We will describe the Linux environment so that participants can start to utilize command-line tools and feel comfortable using a text-based way of interacting with a computer. We will take a problem-solving approach, drawing on types of tasks commonly encountered by Linux users when processing text files. The training room is located on the first floor and there is currently no wheelchair or level access available to this level. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here. |